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ruochiz edited this page Feb 22, 2021 · 18 revisions

Welcome to the Higashi wiki!

Higashi ~ logo ~ Wiki

Toggle table of contents Pages 28

Home
Change Log
Citing Higashi
Configure the parameters
Configure the parameters for Fast Higashi
Contact map style configuration
Dataset selection
Embeddings visualization
Fast Higashi Gallery
Fast Higashi Usage
Higashi Requirements
Higashi Usage
Higashi Usage API
Higashi vis
Higashi vis Usage
Input Files
Known Issues
List of scHi C datasets
Navigate the analysis results
Other components
Output of Higashi analysis
Output of Higashi main
Runtime of Fast Higashi
Runtime of Higashi
Single cell A B compartment calling
Single cell TAD calling
Synchronized navigation of contact maps
Visualization of analysis results

Higashi

Introduction
Installation

Higashi-main

Input files
Usage (CLI)
Usage (API)
Output of Higashi-main
Runtime of Higashi

Higashi-analysis (CLI only for now)

Single cell TAD calling
Single cell A/B compartment calling
Output of Higashi-analysis

Higashi-vis

Configure the Higashi-vis
Launch the service
Navigate the analysis results

Fast-Higashi

Input files
Usage (API)
[Fast-Higashi initialized Higashi (Under construction)]
Runtime of Fast-Higashi

Tutorials

Fast-Higashi Gallery
4DN sci-Hi-C (Kim et al.)
Ramani et al.

General

Known issues
Change log
FAQ
Citing Higashi
List of scHi-C datasets

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